Performs fastq alignment to a fasta reference using using gem3-mapper
meta
:map
Groovy Map containing reference/index information e.g. [ id:‘test’ ]
gem
:file
GEM3 genome index files
*.{gem}
meta2
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
fastq
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
*.{fastq,fq,fastq.gz,fq.gz}
sort_bam
:boolean
use samtools sort (true) or samtools view (false)
true or false
bam
*.bam
Sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
versions_gem3
${task.process}
:string
The name of the process
gem3-mapper
The name of the tool
gem-mapper --version 2>&1 | sed 's/v//'
:eval
The expression to obtain the version of the tool
versions
The GEM indexer (v3).
